Modeling, Information Technology and Bioinformatics


One of the biggest challenges of the CSBi Technology Platform is to develop the informatics infrastructure required for systems biology research. The Modeling, Information Technology and Bioinformatics (MIB) Core strives to create integrated informatics infrastructure that supports the computational demands and modeling needs of the CSBi Technology Platform. One of the first goals of the MIB has been to build a flexible, capable, and robust information technology (IT) infrastructure for the CSBi researchers. The foundation of the IT infrastructure is a data storage and network architecture designed to handle the high volume of data generated and used by systems biology researchers. In addition, the Core provides software tools and web-accessible services to support systems biology research.


The MIB Core provides access and support for software tools needed for systems biology, including software development and model building. The network, computing and storage resources of the HPC Core are essential to support the MIB Core resources.


Training and assistance with the software tools is provided by CSBi staff (see the individual technology cores).


CSBi provides a link to groups and labs that are at the cutting edge of data analysis and modeling and access to software such as Matlab, Spotfire and S-Plus. For more information please email

Data-sharing software

Systems Biology Markup Language

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reactions networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology. Advances in biotechnology are leading to larger, more complex models. The systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.

Modeler’s Notebook and Datastore

MOdelers NOtebook and Datastore (MONOD), is an open source software package for organizing biological knowledge. Monod helps researchers structure natural language information in ways that facilitate its incorporation into quantitative and formal qualitative representations. Monod also supports communication and collaboration among researchers working on and using particular models. Although it is now best suited to facilitate model building, Monod may be extensible to become a general laboratory notebook and distributed knowledge annotation system.